I don't want to implement any extra functions that are not directly related to Automatic Post Tagger, sorry. Although this would be a nice feature for my other (still imaginary) plugin which will work with taxonomies in general.

Why don't you "physically" delete the unwanted tags? You don't have to remove them manually from each post, you can delete them from this page: /wp-admin/edit-tags.php. These tags won't appear in any of your posts anymore if you do this.

Well, if the tag has a specific format I guess that it could removed after importing a post by using a regular expression. There might be a WP hook that would trigger the tag-removing function or a cron could be used if posts are not being imported via the WP import tool.

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